Cracking the code...

Our scientists have cracked a code underlying recognition of
RNA molecules by a superfamily of RNA-binding proteins called penta-tricopeptide repeat (PPR) proteins.
This opens the way to destroying or correcting defective gene products, such as those that cause genetic disorders in humans.

Downloads/Software/Databases available at this centre.

Most of this software uses Java WebStart as a delivery mechanism. Some of the
software has been packaged with a windows Installer. And there are equivalent Application Packages for Mac here

If you would prefer a Windows Installer/Mac Application for some of the software but can't find it here or if - heaven forbid! - you find a bug in any of the software then just send us a email at ian.castleden [at] uwa.edu.au.

"Debugging is twice as hard as writing the code in the first place.
Therefore, if you write the code as cleverly as possible, you are,
by definition, not smart enough to debug it." - Brian W. Kernighan

GC/MS based metabolomics has been used for many aspects of biological studies, but data processing has been problematic due to the frame shifting among chromatograms. We developed a web based program using the jython scripting language to process GC/MS metabolomics data. This program, IDAlgin, can align metabolite peaks by their identifications, thus overcome retention time shifting caused misalignment. This program is useful for both targeted and non-targeted metabolite profiling analysis. GC/MS data is first processed using AMDIS (Automated mass spectral deconvolution and identification system) for deconvolution and identification with existing or custom made libraries. The peak area or integrated signal of each metabolite from all chromatograms identified by AMDIS is then aligned regardless of retention time. The identification of metabolites can be precisely controlled by using AMDIS algorithm incorporating retention index in the deconvolution process. Unknown metabolites are included in the library by assigning them defined identifiers. Alignment quality is controlled by user defined parameters including signal to noise ratio (S/N), difference of retention time or difference of retention index. Alignment can utilize either TIC or integrated signal of metabolite aligning to metabolite name, ID or CAS number. The aligned result can be normalized to a defined internal standard or any metabolite presented in the analysis and can be exported as an Excel spreadsheet for chemometric analysis. This program has potential to be used as a tool to perform large online metabolomics data analysis.

A simple Windows program for combining multiple mzData files into one.

mz2mgf

mz2mgf is a small program to convert mzData files to MGF (current version is 1.3.5). NEW! will convert BioTools xml files too!

Application notes: mz2mgf was choking on our 1.5Gb mzData files so we junked the internally provided java XML parser in favour of an XML PullParser kindly written by Aleksander Slominski (see also here). It's much faster and does not choke on even 3Gb files... oh yes!

A plugin (expa-plugin.jar) for reading .expa files into cytoscape can be found here.
Download and save this jar file into your cytoscape's plugin directory (the directory is called plugins) -- and restart cytoscape. It is compiled against version
2.5 of cytoscape.

dat2mgf

BrukerBuster

A small program to copy a directory tree generated by Bruker into a layout more suitable for reading by...
Windows installer:
download
(Windows only - and you'll still need a Java virtual machine 1.5 or better installed).
Web Start FAQThis work is licenced under a Creative Commons Licence.

Web Equations

Insert equations into your webpages simply and easily! Simple step-by-step instructions on
how to add an equation to your website (no downloads required... and you can even be javascript free!)
Test your LaTeX skills here